Published March 21, 2023 | Version v1
Data paper Open

Sub-micro- and nano-sized polyethylene terephthalate deconstruction with engineered protein nanopores

Creators

  • 1. Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.
  • 2. Departamento de Bioquímica y Biología Molecular, Facultades de Medicina, Biología y Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain.
  • 3. Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain.
  • 4. Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
  • 5. Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain
  • 6. Departamento de Bioquímica y Biología Molecular, Facultades de Medicina, Biología y Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
  • 7. Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain

Description

The authors declare that the main data supporting the findings of this study are available within the paper and related Supplementary Information, Supplementary Data and Source Data files. The molecular simulations, the Molecular Dynamics Simulations, and the quantum mechanical minimizations will be deposited at Zenodo (zenodo/Supplementary raw datasets_1.tar.gz). To use the archive, download the file, and extract its contents to a local directory using appropriate software. The directory will contain separate folders for each type of simulation, along with input and output files.

Abstract

The identification or design of biocatalysts to mitigate the accumulation of plastics, including sub-micro- and nano-sized polyethylene terephthalate (nPET), is becoming a global challenge. Here we computationally incorporated two hydrolytic active sites with geometries similar to that of Idionella sakaiensis PET hydrolase, to fragaceatoxin C (FraC), a membrane pore-forming protein. FraCm1/m2 could be assembled into octameric nanopores (7.0 nm high × 1.6–6.0 nm entry), which deconstructed (40 °C, pH 7.0) nPET from GoodFellow, commodities and plastic bottles. FraCm1 and FraCm2 degrade nPET by endo- and exo-type chain scission. While FraCm1 produces bis(2-hydroxyethyl) terephthalate as the main product, FraCm2 yields a high diversity of oligomers and terephthalic acid. Mechanistic and biochemical differences with benchmark PET hydrolases, along with pore and nPET dynamics, suggest that these pore-forming protein catalytic nanoreactors do not deconstruct macro-PET but are promising in nanotechnology for filtering, capturing and breaking down nPET, for example, in wastewater treatment plants.

Files

Files (33.6 GB)

Name Size Download all
md5:f5d639c48b2128db15eb8e4077d7d5b5
1.7 GB Download
md5:a889c2718ec568c7df851ca281995b9e
12.3 GB Download
md5:80acada6088fe6dc3955746cb3feff3f
19.6 GB Download
md5:3815111b3920cd3373b12625df961e3f
7.4 MB Download